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Tang J, Wang Y, Ma J, Chen Y, Chen M. Activation of peroxymonosulfate by sustainable biomass-based carbon nanotubes for controlling the spread of plant viruses in water environments. J Environ Sci (China) 2025; 149:99-112. [PMID: 39181682 DOI: 10.1016/j.jes.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 08/27/2024]
Abstract
With the increasing demand for water in hydroponic systems and agricultural irrigation, viral diseases have seriously affected the yield and quality of crops. By removing plant viruses in water environments, virus transmission can be prevented and agricultural production and ecosystems can be protected. But so far, there have been few reports on the removal of plant viruses in water environments. Herein, in this study, easily recyclable biomass-based carbon nanotubes catalysts were synthesized with varying metal activities to activate peroxymonosulfate (PMS). Among them, the magnetic 0.125Fe@NCNTs-1/PMS system showed the best overall removal performance against pepper mild mottle virus, with a 5.9 log10 removal within 1 min. Notably, the key reactive species in the 0.125Fe@NCNTs-1/PMS system is 1O2, which can maintain good removal effect in real water matrices (river water and tap water). Through RNA fragment analyses and label free analysis, it was found that this system could effectively cleave virus particles, destroy viral proteins and expose their genome. The capsid protein of pepper mild mottle virus was effectively decomposed where serine may be the main attacking sites by 1O2. Long viral RNA fragments (3349 and 1642 nt) were cut into smaller fragments (∼160 nt) and caused their degradation. In summary, this study contributes to controlling the spread of plant viruses in real water environment, which will potentially help protect agricultural production and food safety, and improve the health and sustainability of ecosystems.
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Affiliation(s)
- Jian Tang
- College of Resources and Environment, Yangtze University, Wuhan 430100, China; Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yujie Wang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jun Ma
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yujie Chen
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; School of Geography and Tourism, Chongqing Normal University, Chongqing 400714, China
| | - Ming Chen
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China.
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Yang Z, Li G, Zhang Y, Li F, Zhou T, Ye J, Wang X, Zhang X, Sun Z, Tao X, Wu M, Wu J, Li Y. Crop antiviral defense: Past and future perspective. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2680-3. [PMID: 39190125 DOI: 10.1007/s11427-024-2680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]
Abstract
Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.
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Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangyao Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wu Y, Liu N, Zheng C, Li D, Li S, Wu J, Zhao S. Insights into the Complexity and Functionality of Plant Virus Protein Phosphorylation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:598-610. [PMID: 38814574 DOI: 10.1094/mpmi-04-24-0034-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Phosphorylation, the most extensive and pleiotropic form of protein posttranslation modification, is central to cellular signal transduction. Throughout the extensive co-evolution of plant hosts and viruses, modifications to phosphorylation have served multiple purposes. Such modifications highlight the evolutionary trajectories of viruses and their hosts, with pivotal roles in regulation and refinement of host-virus interactions. In plant hosts, protein phosphorylation orchestrates immune responses, enhancing the activities of defense-related proteins such as kinases and transcription factors, thereby strengthening pathogen resistance in plants. Moreover, phosphorylation influences the interactions between host and viral proteins, altering viral spread and replication within host plants. In the context of plant viruses, protein phosphorylation controls key aspects of the infection cycle, including viral protein functionality and the interplay between viruses and host plant cells, leading to effects on viral accumulation and dissemination within plant tissues. Explorations of the nuances of protein phosphorylation in plant hosts and their interactions with viruses are particularly important. This review provides a systematic summary of the biological roles of the proteins of plant viruses carrying diverse genomes in regulating infection and host responses through changes in the phosphorylation status. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yuansheng Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Na Liu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengxu Zheng
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongyuan Li
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shanshan Li
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shanshan Zhao
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Liu H, Deng B, Chen FH, Suo JQ, Ouyang GC, Lu HL, Chen DS, Meng X. Effector enrichment by Candidatus Liberibacter promotes Diaphorina citri feeding via Jasmonic acid pathway suppression. PEST MANAGEMENT SCIENCE 2024; 80:4013-4023. [PMID: 38554028 DOI: 10.1002/ps.8107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/09/2024] [Accepted: 03/30/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Citrus huanglongbing (HLB) is a devastating disease caused by Candidatus Liberibacter asiaticus (CLas) that affects the citrus industry. In nature, CLas relies primarily on Diaphorina citri Kuwayama as its vector for dissemination. After D. citri ingests CLas-infected citrus, the pathogen infiltrates the insect's body, where it thrives, reproduces, and exerts regulatory control over the growth and metabolism of D. citri. Previous studies have shown that CLas alters the composition of proteins in the saliva of D. citri, but the functions of these proteins remain largely unknown. RESULTS In this study, we detected two proteins (DcitSGP1 and DcitSGP3) with high expression levels in CLas-infected D. citri. Quantitative PCR and Western blotting analysis showed that the two proteins were highly expressed in the salivary glands and delivered into the host plant during feeding. Silencing the two genes significantly decreased the survival rate for D. citri, reduced phloem nutrition sucking and promoted jasmonic acid (JA) defenses in citrus. By contrast, after overexpressing the two genes in citrus, the expression levels of JA pathway-associated genes decreased. CONCLUSION Our results suggest that CLas can indirectly suppress the defenses of citrus and support feeding by D. citri via increasing the levels of effectors in the insect's saliva. This discovery facilitates further research into the interaction between insect vectors and pathogens. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Hao Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Bin Deng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Feng-Hao Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Jia-Qi Suo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Ge-Cheng Ouyang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Hui-Lin Lu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Da-Song Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Xiang Meng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
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Liu X, Zhang Y, Zou Y, Yan C, Chen J. Recent Advances and Outlook of Benzopyran Derivatives in the Discovery of Agricultural Chemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12300-12318. [PMID: 38800848 DOI: 10.1021/acs.jafc.3c09244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Scaffold structures, new mechanisms of action, and targets present enormous challenges in the discovery of novel pesticides. The discovery of new scaffolds is the basis for the continuous development of modern agrochemicals. Identification of a good scaffold such as triazole, carbamate, methoxy acrylate, pyrazolamide, pyrido-pyrimidinone mesoionic, and bisamide often leads to the development of a new series of pesticides. In addition, pesticides with the same target, including the inhibitors of succinate dehydrogenase (SDH), oxysterol-binding-protein, and p-hydroxyphenyl pyruvate dioxygenase (HPPD), may have the same or similar scaffold structure. Recent years have witnessed significant progress in the discovery of new pesticides using natural products as scaffolds or bridges. In recent years, there have been increasing reports on the application of natural benzopyran compounds in the discovery of new pesticides, especially osthole and coumarin. A systematic and comprehensive review of benzopyran active compounds in the discovery of new agricultural chemicals is helpful to promote the discussion and development of benzopyran active compounds. Therefore, this work systematically reviewed the research and application of benzopyran derivatives in the discovery of agricultural chemicals, summarized the antiviral, herbicidal, antibacterial, fungicidal, insecticidal, nematicidal and acaricidal activities of benzopyran active compounds, and discussed the structural-activity relationship and mechanism of action. In addition, some active fragments were recommended to further optimize the chemical structure of benzopyran active compounds based on reference information.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yong Zhang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yue Zou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Chongchong Yan
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jixiang Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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6
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Hussain A, Khan AA, Aslam MQ, Nazar A, Zaman N, Amin A, Mahmood MA, Mukhtar MS, Rahman HUU, Farooq M, Saeed M, Amin I, Mansoor S. Comparative analysis, diversification, and functional validation of plant nucleotide-binding site domain genes. Sci Rep 2024; 14:11930. [PMID: 38789717 PMCID: PMC11126693 DOI: 10.1038/s41598-024-62876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/22/2024] [Indexed: 05/26/2024] Open
Abstract
Nucleotide-binding site (NBS) domain genes are one of the superfamily of resistance genes involved in plant responses to pathogens. The current study identified 12,820 NBS-domain-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes are classified into 168 classes with several novel domain architecture patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR, etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2, etc.) and unique (highly specific to species; OG80, OG82, etc.) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6, and OG15 in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to cotton leaf curl disease (CLCuD). The genetic variation between susceptible (Coker 312) and tolerant (Mac7) Gossypium hirsutum accessions identified several unique variants in NBS genes of Mac7 (6583 variants) and Coker312 (5173 variants). The protein-ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of the cotton leaf curl disease virus. The silencing of GaNBS (OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful in understanding the plant adaptation mechanism.
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Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan.
| | - Aqsa Anwer Khan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Aquib Nazar
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Nadir Zaman
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Ayesha Amin
- Department of Biological Sciences, Superior University, Lahore, 54000, Pakistan
| | - Muhammad Arslan Mahmood
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - M Shahid Mukhtar
- Biosystems Research Complex, Department of Genetics & Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Hafiz Ubaid Ur Rahman
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammed Farooq
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Muhammed Saeed
- Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau Abteilung Phytopathologie, Paul-Ehrlich-Straße 22, 67653, Kaiserslautern, Germany
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- Jamil ur Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 74000, Pakistan.
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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8
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2024; 51:367-378. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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9
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Liang Y, Wan J, Zhang X, Li K, Su J, Gui M, Li Y, Liu Y. Comprehensive phytohormone metabolomic and transcriptomic analysis of tobacco (Nicotiana tabacum) infected by tomato spotted wilt virus (TSWV). Virus Res 2024; 342:199334. [PMID: 38325524 PMCID: PMC10875290 DOI: 10.1016/j.virusres.2024.199334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Tomato spotted wilt virus (TSWV) is ranked among the top 10 most destructive viruses globally. It results in abnormal leaf growth, stunting, and even death, significantly affecting crop yield and quality. Phytohormones play a crucial role in regulating plant-virus interactions. However, there is still limited research on the effect of TSWV on phytohormone levels, particularly growth hormones and genes involved in the phytohormone pathway. In our study, we combined phytohormone metabolomics and transcriptomics to examine the impact of TSWV infection on phytohormone content and gene expression profile. Metabolomic results showed that 41 metabolites, including major phytohormones and their precursors and derivatives were significantly altered after 14 days of TSWV inoculation tobacco plants cvK326, with 31 being significantly increased and 10 significantly reduced. Specifically, the levels of abscisic acid (ABA) and jasmonoyl-isoleucine (JA-Ile) were significantly reduced. The levels of indole-3-acetic acid (IAA) have remained unchanged. However, the levels of cytokinin isopentenyladenine (iP) and salicylic acid (SA) significantly increased. The transcriptome analysis revealed 2,746 genes with significant changes in expression. Out of these, 1,072 genes were significantly downregulated, while 1,674 genes were significantly upregulated. Among them, genes involved in ABA synthesis and signaling pathways, such as 9-cis-epoxycarotenoid dioxygenase (NCED), protein phosphatase 2C (PP2C), serine/threonine-protein kinase (SnRK2), and abscisic acid responsive element binding factor (ABF), exhibited significant downregulation. Additionally, expression of the lipoxygenase gene LOX, Jasmonate ZIM domain-containing protein gene JAZ, and transcription factor gene MYC were significantly down-regulated. In the cytokinin pathway, while there were no significant changes in the expression of the cytokinin synthesis genes, a significant downregulation of transcriptionally active factor type-B response regulators (type-B RRs) was observed. In terms of SA synthesis and signaling pathways, the isochorismate synthase gene ICS1 and the pathogenesis-related gene PR1 were significantly upregulated. These results can strengthen the theoretical foundation for understanding the interaction between TSWV and tobacco and provide new insights for the future prevention and control of TSWV.
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Affiliation(s)
- Yanping Liang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; Institute of Horticultural Research,Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jinfeng Wan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; College of Food, Drug and Health, Yunnan Vocational and Technical College of Agriculture, Kunming 6 50212, China
| | - Xin Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Kunming Li
- Institute of Horticultural Research,Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jun Su
- Institute of Horticultural Research,Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Min Gui
- Institute of Horticultural Research,Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Yongzhong Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China.
| | - Yating Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China.
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10
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Hamim I, Sipes B, Wang Y. Editorial: Detection, characterization, and management of plant pathogens. FRONTIERS IN PLANT SCIENCE 2024; 15:1354042. [PMID: 38414641 PMCID: PMC10897511 DOI: 10.3389/fpls.2024.1354042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Affiliation(s)
- Islam Hamim
- Department of Plant Pathology, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Brent Sipes
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yanan Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
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11
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Metwally RA, Taha MA, El-Moaty NMA, Abdelhameed RE. Attenuation of Zucchini mosaic virus disease in cucumber plants by mycorrhizal symbiosis. PLANT CELL REPORTS 2024; 43:54. [PMID: 38315215 PMCID: PMC10844420 DOI: 10.1007/s00299-023-03138-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE Arbuscular mycorrhizal fungi generated systemic acquired resistance in cucumber to Zucchini yellow mosaic virus, indicating their prospective application in the soil as a sustainable, environmentally friendly approach to inhibit the spread of pathogens. The wide spread of plant pathogens affects the whole world, causing several plant diseases and threatening national food security as it disrupts the quantity and quality of economically important crops. Recently, environmentally acceptable mitigating practices have been required for sustainable agriculture, restricting the use of chemical fertilizers in agricultural areas. Herein, the biological control of Zucchini yellow mosaic virus (ZYMV) in cucumber (Cucumis sativus L.) plants using arbuscular mycorrhizal (AM) fungi was investigated. Compared to control plants, ZYMV-infected plants displayed high disease incidence (DI) and severity (DS) with various symptoms, including severe yellow mosaic, mottling and green blisters of leaves. However, AM fungal inoculation exhibited 50% inhibition for these symptoms and limited DS to 26% as compared to non-colonized ones. The detection of ZYMV by the Enzyme-Linked Immunosorbent Assay technique exhibited a significant reduction in AM-inoculated plants (5.23-fold) compared with non-colonized ones. Besides, mycorrhizal root colonization (F%) was slightly reduced by ZYMV infection. ZYMV infection decreased all growth parameters and pigment fractions and increased the malondialdehyde (MDA) content, however, these parameters were significantly enhanced and the MDA content was decreased by AM fungal colonization. Also, the protein, proline and antioxidant enzymes (POX and CAT) were increased with ZYMV infection with more enhancements due to AM root colonization. Remarkably, defence pathogenesis-related (PR) genes such as PR-a, PR-b, and PR-10 were quickly expressed in response to AM treatment. Our findings demonstrated the beneficial function of AM fungi in triggering the plant defence against ZYMV as they caused systemic acquired resistance in cucumber plants and supported their potential use in the soil as an environment-friendly method of hindering the spread of pathogenic microorganisms sustainably.
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Affiliation(s)
- Rabab A Metwally
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Mohamed A Taha
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Nada M Abd El-Moaty
- Microbiology Department, Soil, Water and Environment Research Institute (SWERI), Agricultural Research Center, Giza, Egypt
| | - Reda E Abdelhameed
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
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12
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Song L, Zhang D, Liu T, Jiang C, Li B, Li C, Shen L, Li Y, Wang F, Jiao Y, Yang J. Non-transgenic, PAMAM co-delivery DNA of interactive proteins NbCRVP and NbCalB endows Nicotiana benthamiana with a stronger antiviral effect to RNA viruses. J Nanobiotechnology 2024; 22:23. [PMID: 38191434 PMCID: PMC10773047 DOI: 10.1186/s12951-023-02252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Viral diseases continue to pose a major threat to the world's commercial crops. The in-depth exploration and efficient utilization of resistance proteins have become crucial strategies for their control. However, current delivery methods for introducing foreign DNA suffer from host range limitations, low transformation efficiencies, tissue damage, or unavoidable DNA integration into the host genome. The nanocarriers provides a convenient channel for the DNA delivery and functional utilization of disease-resistant proteins. RESULTS In this research, we identified a cysteine-rich venom protein (NbCRVP) in Nicotiana benthamiana for the first time. Virus-induced gene silencing and transient overexpression clarified that NbCRVP could inhibit the infection of tobacco mosaic virus, potato virus Y, and cucumber mosaic virus, making it a broad-spectrum antiviral protein. Yeast two-hybrid assay, co-immunoprecipitation, and bimolecular fluorescence complementation revealed that calcium-dependent lipid-binding (CaLB domain) family protein (NbCalB) interacted with NbCRVP to assist NbCRVP playing a stronger antiviral effect. Here, we demonstrated for the first time the efficient co-delivery of DNA expressing NbCRVP and NbCalB into plants using poly(amidoamine) (PAMAM) nanocarriers, achieving stronger broad-spectrum antiviral effects. CONCLUSIONS Our work presents a tool for species-independent transfer of two interacting protein DNA into plant cells in a specific ratio for enhanced antiviral effect without transgenic integration, which further demonstrated new strategies for nanocarrier-mediated DNA delivery of disease-resistant proteins.
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Affiliation(s)
- Liyun Song
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- College of Agriculture and Forestry Science and Technology, Weifang Vocational College, Weifang, 262737, China
| | - Daoshun Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianbo Liu
- Tobacco Research Institute of Hunan Province, Hunan, 410004, China
| | - Changqing Jiang
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, China
| | - Bin Li
- Sichuan Tobacco Company, Chengdu, 610000, China
| | - Changquan Li
- Liupanshui City Company of Guizhou Tobacco Company, Liupanshui, 553000, Guizhou, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Yubing Jiao
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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13
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Lutz T, Jaeckel M, Hadeler B, Heinze C. Fast preparation of high-quality viral dsRNA from fungal tissue by commercial nucleic acid extraction kits. J Virol Methods 2023; 322:114832. [PMID: 37858808 DOI: 10.1016/j.jviromet.2023.114832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The genomes of most known mycoviruses consist of double stranded RNA (dsRNA) or single stranded RNA (ssRNA). Therefore, for all aspects of mycovirology, the research is highly dependent on the quality and quantity of RNA either by the extraction of genomic dsRNA or dsRNA as a replicating intermediate. A common procedure to extract dsRNA is its binding on a cellulose matrix after a phenol/chloroform purification step. A commercial kit for dsRNA extraction facilitated the researchers´ daily work, but is not available anymore. To extract nucleic acids in a standardized good quality and quantity from small amounts of starting material, we compared commercial kits for gDNA extraction to the kits for RNA extraction using fungal material with a high and a low virus titer. Here we show that viral dsRNA can be extracted using commercial gDNA kits from fungal tissue with a high and a low virus titer in the same quality and quantity as it was done with the discontinued dsRNA extraction kit.
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Affiliation(s)
- Tobias Lutz
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Mareike Jaeckel
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Birgit Hadeler
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Cornelia Heinze
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609 Hamburg, Germany.
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14
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Zhang H, Hu Q. TOM1 family conservation within the plant kingdom for tobacco mosaic virus accumulation. MOLECULAR PLANT PATHOLOGY 2023; 24:1385-1399. [PMID: 37443447 PMCID: PMC10576174 DOI: 10.1111/mpp.13375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/03/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
The susceptibility factor TOBAMOVIRUS MULTIPLICATION 1 (TOM1) is required for efficient multiplication of tobacco mosaic virus (TMV). Although some phylogenetic and functional analyses of the TOM1 family members have been conducted, a comprehensive analysis of the TOM1 homologues based on phylogeny from the most ancient to the youngest representatives within the plant kingdom, analysis of support for tobamovirus accumulation and interaction with other host and viral proteins has not been reported. In this study, using Nicotiana benthamiana and TMV as a model system, we functionally characterized the TOM1 homologues from N. benthamiana and other plant species from different plant lineages. We modified a multiplex genome editing tool and generated a sextuple mutant in which TMV multiplication was dramatically inhibited. We showed that TOM1 homologues from N. benthamiana exhibited variable capacities to support TMV multiplication. Evolutionary analysis revealed that the TOM1 family is restricted to the plant kingdom and probably originated in the Chlorophyta division, suggesting an ancient origin of the TOM1 family. We found that the TOM1 family acquired the ability to promote TMV multiplication after the divergence of moss and spikemoss. Moreover, the capacity of TOM1 orthologues from different plant species to promote TMV multiplication and the interactions between TOM1 and TOM2A and between TOM1 and TMV-encoded replication proteins are highly conserved, suggesting a conserved nature of the TOM2A-TOM1-TMV Hel module in promoting TMV multiplication. Our study not only revealed a conserved nature of a gene module to promote tobamovirus multiplication, but also provides a valuable strategy for TMV-resistant crop development.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Qun Hu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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15
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Yang FX, Ma YY, Wu YP, Zhao GK, Li YP, Li ZJ, Li XM, Li YK, Wang WG, Zhou M, Kong GH, Hu QF. Extraction and characterization of anti-virus anthraquinones from Nicotiana tabacum-derived Aspergillus oryzae YNCA1220. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 196:105613. [PMID: 37945230 DOI: 10.1016/j.pestbp.2023.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 11/12/2023]
Abstract
In this study, seven novel anthraquinones (1-7) and four described anthraquinones (8-11) were purified from Nicotiana tabacum-derived Aspergillus oryzae YNCA1220. It is worth noting that only analogs of 4 and 5 have been reported as natural products to date, while the nuclei of compounds 1-3, 6 and 7 were isolated for the first time in nature. Among them, compounds 1-3 bear an unusual anthra[2,3-b]furan-9,10-dione nucleus, 4 and 5 possess a rare 3-methyl-1H-pyrrol-2-yl substituent, and 6 and 7 are new framework anthraquinones bearing a 6-methyl-1,7-dihydro-2H-azepin-2-one ring. Interestingly, the in vivo assays indicated that 1, 4 and 5 had inactivation effects against tobacco mosaic virus (TMV) with inhibition rates of 41.6%, 55.4% and 38.6%, respectively, at a concentration of 50 μg/mL, which were better than that of the positive control agent, ningnanmycin (33.8%). Compounds 1, 4 and 5 also had protective effects with inhibition rates of 48.7%, 60.2% and 43.5% at the same concentration, while 4 had a better curative effect than ningnanmycin at a concentration of 100 μg/mL. In addition, mechanistic studies also revealed that a potent direct effect on TMV, the induction of SAR in tobacco plants, and the effective regulation of defense enzymes, defense genes, and defense hormones may be the reasons for the significant effects of 4 against TMV. At the same time, downregulation of the expression of total NtHsp70 protein by inhibiting the related Hsp70 genes may also be involved in tobacco resistance to TMV. To evaluate whether compounds have broader antiviral activities, the antirotavirus activities of new isolates were also evaluated and found to be highly effective with a therapeutic index (TI) value ranging from 11.6 to 17.7. This study suggests that the above anthraquinone compounds, particularly 4, have broad spectrum antiviral activities. The successful isolation and structure identification of the above anthraquinones provide new materials for the screening of anti-TMV agents and contribute to the improved utilization of N. tabacum-derived fungi.
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Affiliation(s)
- Feng-Xian Yang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China; Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, PR China
| | - Yue-Yu Ma
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China
| | - Yu-Ping Wu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China
| | - Gao-Kun Zhao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China
| | - Yong-Ping Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China
| | - Zhen-Jie Li
- Yunnan Key Laboratory of Tobacco Chemistry, China Tobacco Yunnan Industrial Co., Ltd., Kunming 650031, PR China
| | - Xue-Mei Li
- Yunnan Key Laboratory of Tobacco Chemistry, China Tobacco Yunnan Industrial Co., Ltd., Kunming 650031, PR China
| | - Yin-Ke Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China; Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China
| | - Wei-Guang Wang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China
| | - Min Zhou
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China
| | - Guang-Hui Kong
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China.
| | - Qiu-Fen Hu
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, PR China; Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650031, PR China.
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16
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Naveed H, Islam W, Jafir M, Andoh V, Chen L, Chen K. A Review of Interactions between Plants and Whitefly-Transmitted Begomoviruses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3677. [PMID: 37960034 PMCID: PMC10648457 DOI: 10.3390/plants12213677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The transmission of plant viruses from infected to healthy host plants is a process in which insects play a major role, using various transmission strategies. Environmental factors have an impact on the transmission of viruses and the subsequent development of infections or diseases. When viruses are successful, plant virus diseases can reach epidemic proportions. Many plants across different regions are vulnerable to viral infections transmitted by the whitefly vector. Begomoviruses, which are transmitted by whiteflies, represent a significant threat to agriculture worldwide. The review highlights the mechanisms of virus acquisition and transmission by whiteflies and explores the factors influencing these interactions. Understanding the impacts of these changes is crucial for managing the spread of pests and mitigating damage to crops. It underscores the need for continued research to elucidate the mechanisms driving plant-insect-virus interactions and to identify new approaches for sustainable pest management.
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Affiliation(s)
- Hassan Naveed
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China;
| | - Waqar Islam
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;
| | - Muhammad Jafir
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China;
| | - Vivian Andoh
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China;
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China;
| | - Keping Chen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China;
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17
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Guo Q, Sun Y, Ji C, Kong Z, Liu Z, Li Y, Li Y, Lai H. Plant resistance to tomato yellow leaf curl virus is enhanced by Bacillus amyloliquefaciens Ba13 through modulation of RNA interference. Front Microbiol 2023; 14:1251698. [PMID: 37869663 PMCID: PMC10587425 DOI: 10.3389/fmicb.2023.1251698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Tomato yellow leaf curl virus (TYLCV), which is a typical member of the genus Begomovirus, causes severe crop yield losses worldwide. RNA interference (RNAi) is an important antiviral defense mechanism in plants, but whether plant beneficial microbes used as biocontrol agents would modulate RNAi in defense against TYLCV remains unclear. Methods Here, we employed whole-transcriptome, bisulfite, and small RNA sequencing to decipher the possible role of Bacillus amyloliquefaciens Ba13 as a bacterial biocontrol agent against TYLCV in RNAi modulation. Results Potted tomato plants were exposed to whiteflies for natural viral infection 14 days after bacterial inoculation. Compared with non-inoculated controls, the abundance of TYLCV gene in the leaves of inoculated plants decreased by 70.1% at 28 days post-infection, which mirrored the pattern observed for plant disease index. The expression of the ARGONAUTE family genes (e.g., AGO3, AGO4, AGO5, and AGO7) involved in antiviral defense markedly increased by 2.44-6.73-fold following bacterial inoculation. The methylation level at CpG site 228 (in the open reading frame region of the RNA interference suppressing gene AV2) and site 461 (in the open reading frame regions of AV1 and AV2) was 183.1 and 63.0% higher in inoculated plants than in non-inoculated controls, respectively. The abundances of 10 small interfering RNAs matched to the TYLCV genome were all reduced in inoculated plants, accompanied by enhancement of photosystem and auxin response pathways. Discussion The results indicate that the application of Ba. amyloliquefaciens Ba13 enhances plant resistance to TYLCV through RNAi modulation by upregulating RNAi-related gene expression and enhancing viral genome methylation.
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Affiliation(s)
- Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Yifan Sun
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Chenglong Ji
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Zirong Kong
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Zhe Liu
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Yulong Li
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
| | - Yunzhou Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, China
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18
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Ruiz‐Ramón F, Rodríguez‐Sepúlveda P, Bretó P, Donaire L, Hernando Y, Aranda MA. The tomato calcium-permeable channel 4.1 (SlOSCA4.1) is a susceptibility factor for pepino mosaic virus. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2140-2154. [PMID: 37448155 PMCID: PMC10502756 DOI: 10.1111/pbi.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
The hyperosmolality-gated calcium permeable channel 4.1 (OSCA4.1) belongs to an evolutionarily conserved small family of mechano-sensitive channels. OSCA members may represent key players in plant resistance to drought and to pathogen infection but are scarcely studied. After screening for resistance to pepino mosaic virus (PepMV) a collection of 1000 mutagenized tomato families, we identified a mutant showing no symptoms and reduced virus accumulation. Resistance was mapped to chromosome 2 between positions 46 309 531 to 47 044 163, where a missense mutation caused the putative truncation of the OSCA4.1 protein. A CRISPR/Cas9 slosca4.1 mutant was resistant to PepMV, but not to tobacco mosaic virus or potato virus X. Inoculation of mutant and wild type tomato protoplasts showed that resistance was expressed in single cells, suggesting a role for SlOSCA4.1 in early viral function(s); congruently, SlOSCA4.1 re-localized to structures reminiscent of viral replication complexes. We propose that SlOSCA4.1 contributes to the correct regulation of the Ca2+ homeostasis necessary for optimal PepMV infection. PepMV is a pandemic virus that causes significant losses in tomato crops worldwide. In spite of its importance, no tomato-resistant varieties have been deployed yet; the mutant identified here has great potential to breed tomato varieties resistant to PepMV.
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Affiliation(s)
- Fabiola Ruiz‐Ramón
- Abiopep S.L., Parque Científico de MurciaMurciaSpain
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICCampus Universitario de EspinardoMurciaSpain
| | | | - Pau Bretó
- Abiopep S.L., Parque Científico de MurciaMurciaSpain
| | - Livia Donaire
- Abiopep S.L., Parque Científico de MurciaMurciaSpain
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICCampus Universitario de EspinardoMurciaSpain
| | | | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICCampus Universitario de EspinardoMurciaSpain
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Gutiérrez-Jara JP, Vogt-Geisse K, Correa MCG, Vilches-Ponce K, Pérez LM, Chowell G. Modeling the Impact of Agricultural Mitigation Measures on the Spread of Sharka Disease in Sweet Cherry Orchards. PLANTS (BASEL, SWITZERLAND) 2023; 12:3442. [PMID: 37836182 PMCID: PMC10575084 DOI: 10.3390/plants12193442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Sharka is a disease affecting stone fruit trees. It is caused by the Plum pox virus (PPV), with Myzus persicae being one of the most efficient aphid species in transmitting it within and among Prunus orchards. Other agricultural management strategies are also responsible for the spread of disease among trees, such as grafting and pruning. We present a mathematical model of impulsive differential equations to represent the dynamics of Sharka disease in the tree and vector population. We consider three transmission routes: grafting, pruning, and through aphid vectors. Grafting, pruning, and vector control occur as pulses at specific instants. Within the model, human risk perception towards disease influences these agricultural management strategies. Model results show that grafting with infected biological material has a significant impact on the spread of the disease. In addition, detecting infectious symptomatic and asymptomatic trees in the short term is critical to reduce disease spread. Furthermore, vector control to prevent aphid movement between trees is crucial for disease mitigation, as well as implementing awareness campaigns for Sharka disease in agricultural communities that provide a long-term impact on responsible pruning, grafting, and vector control.
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Affiliation(s)
- Juan Pablo Gutiérrez-Jara
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile;
| | - Katia Vogt-Geisse
- Facultad de Ingeniería y Ciencias, Unidad Adolfo Ibáñez, Diagonal Las Torres 2640, Peñalolén, Santiago 7941169, Chile
| | - Margarita C. G. Correa
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile;
| | - Karina Vilches-Ponce
- Facultad de Ciencias Básicas, Universidad Católica del Maule, Avenida San Miguel 3605, Talca 3480112, Chile;
| | - Laura M. Pérez
- Departamento de Física, Universidad de Tarapacá, Casilla 7D, Arica 1000000, Chile;
| | - Gerardo Chowell
- School of Public Health, Georgia State University, Atlanta, GA 30303, USA;
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20
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Salem NM, Jewehan A, Aranda MA, Fox A. Tomato Brown Rugose Fruit Virus Pandemic. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:137-164. [PMID: 37268006 DOI: 10.1146/annurev-phyto-021622-120703] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) is an emerging tobamovirus. It was first reported in 2015 in Jordan in greenhouse tomatoes and now threatens tomato and pepper crops around the world. ToBRFV is a stable and highly infectious virus that is easily transmitted by mechanical means and via seeds, which enables it to spread locally and over long distances. The ability of ToBRFV to infect tomato plants harboring the commonly deployed Tm resistance genes, as well as pepper plants harboring the L resistance alleles under certain conditions, limits the ability to prevent damage from the virus. The fruit production and quality of ToBRFV-infected tomato and pepper plants can be drastically affected, thus significantly impacting their market value. Herein, we review the current information and discuss the latest areas of research on this virus, which include its discovery and distribution, epidemiology, detection, and prevention and control measures, that could help mitigate the ToBRFV disease pandemic.
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Affiliation(s)
- Nida' M Salem
- Department of Plant Protection, School of Agriculture, The University of Jordan, Amman, Jordan;
| | - Ahmad Jewehan
- Applied Plant Genomics Group, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Murcia, Spain
| | - Adrian Fox
- Fera Science, Sand Hutton, York, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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21
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Zhan X, Liu W, Nie B, Zhang F, Zhang J. Cas13d-mediated multiplex RNA targeting confers a broad-spectrum resistance against RNA viruses in potato. Commun Biol 2023; 6:855. [PMID: 37591976 PMCID: PMC10435558 DOI: 10.1038/s42003-023-05205-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
CRISPR-Cas systems endow the bacterial and archaeal species with adaptive immune mechanisms to fend off invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13d has been harnessed to confer the protection against RNA viruses in diverse eukaryotic species. However a vast number of different viruses can potentially infect the same host plant resulting in mixed infection, thus necessitating the generation of crops with broad-spectrum resistance to multiple viruses. Here we report the repurposing of CRISPR/Cas13d coupled with an endogenous tRNA-processing system (polycistronic tRNA-gRNA, PTG) to target the multiple potato RNA viruses. Expression of Cas13d and four different gRNAs were observed in transgenic potato lines expressing the Cas13d/PTG construct. We show that the Cas13d/PTG transgenic plants exhibit resistance to either PVY, PVS, PVX or PLRV alone or two/three viruses simultaneously by reducing viral accumulation in plant cells. In sum, our findings provide an efficient strategy for engineering crops that can simultaneously resist infection by multiple RNA viruses.
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Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenting Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Bihua Nie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
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22
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Jovanović I, Frantová N, Zouhar J. A sword or a buffet: plant endomembrane system in viral infections. FRONTIERS IN PLANT SCIENCE 2023; 14:1226498. [PMID: 37636115 PMCID: PMC10453817 DOI: 10.3389/fpls.2023.1226498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
The plant endomembrane system is an elaborate collection of membrane-bound compartments that perform distinct tasks in plant growth and development, and in responses to abiotic and biotic stresses. Most plant viruses are positive-strand RNA viruses that remodel the host endomembrane system to establish intricate replication compartments. Their fundamental role is to create optimal conditions for viral replication, and to protect replication complexes and the cell-to-cell movement machinery from host defenses. In addition to the intracellular antiviral defense, represented mainly by RNA interference and effector-triggered immunity, recent findings indicate that plant antiviral immunity also includes membrane-localized receptor-like kinases that detect viral molecular patterns and trigger immune responses, which are similar to those observed for bacterial and fungal pathogens. Another recently identified part of plant antiviral defenses is executed by selective autophagy that mediates a specific degradation of viral proteins, resulting in an infection arrest. In a perpetual tug-of-war, certain host autophagy components may be exploited by viral proteins to support or protect an effective viral replication. In this review, we present recent advances in the understanding of the molecular interplay between viral components and plant endomembrane-associated pathways.
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Affiliation(s)
- Ivana Jovanović
- Department of Crop Science, Breeding and Plant Medicine, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Nicole Frantová
- Department of Crop Science, Breeding and Plant Medicine, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Jan Zouhar
- Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
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23
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Sun H, Jing X, Wang C, Wang P, Huang Z, Sun B, Li P, Li H, Zhang C. The Great Game between Plants and Viruses: A Focus on Protein Homeostasis. Int J Mol Sci 2023; 24:12582. [PMID: 37628763 PMCID: PMC10454472 DOI: 10.3390/ijms241612582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Plant viruses are tiny pathogenic obligate parasites that cause significant damage to global crop production. They exploit and manipulate the cellular components of host plants to ensure their own survival. In response, plants activate multiple defense signaling pathways, such as gene silencing and plant hormone signaling, to hinder virus propagation. Growing evidence suggests that the regulation of protein homeostasis plays a vital role in the ongoing battle between plants and viruses. The ubiquitin-proteasome-degradation system (UPS) and autophagy, as two major protein-degradation pathways, are widely utilized by plants and viruses in their arms race. One the one hand, these pathways act as essential components of plant's antiviral defense system by facilitating the degradation of viral proteins; on the other hand, viruses exploit the UPS and autophagy to create a favorable intracellular environment for viral infection. This review aims to provide a comprehensive summary of the events involved in protein homeostasis regulation during viral infection in plants. Gaining knowledge in this area will enhance our understanding of the complex interplay between plants and viruses.
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Affiliation(s)
- Hangjun Sun
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinxin Jing
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chaonan Wang
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengyue Wang
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Ziting Huang
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingjian Sun
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengbai Li
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Honglian Li
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Zhang
- The Engineering Research Center for Plant Health Protection Technology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
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24
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Jiang T, Zhou T. Unraveling the Mechanisms of Virus-Induced Symptom Development in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2830. [PMID: 37570983 PMCID: PMC10421249 DOI: 10.3390/plants12152830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Plant viruses, as obligate intracellular parasites, induce significant changes in the cellular physiology of host cells to facilitate their multiplication. These alterations often lead to the development of symptoms that interfere with normal growth and development, causing USD 60 billion worth of losses per year, worldwide, in both agricultural and horticultural crops. However, existing literature often lacks a clear and concise presentation of the key information regarding the mechanisms underlying plant virus-induced symptoms. To address this, we conducted a comprehensive review to highlight the crucial interactions between plant viruses and host factors, discussing key genes that increase viral virulence and their roles in influencing cellular processes such as dysfunction of chloroplast proteins, hormone manipulation, reactive oxidative species accumulation, and cell cycle control, which are critical for symptom development. Moreover, we explore the alterations in host metabolism and gene expression that are associated with virus-induced symptoms. In addition, the influence of environmental factors on virus-induced symptom development is discussed. By integrating these various aspects, this review provides valuable insights into the complex mechanisms underlying virus-induced symptoms in plants, and emphasizes the urgency of addressing viral diseases to ensure sustainable agriculture and food production.
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Affiliation(s)
| | - Tao Zhou
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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25
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Iturralde Martinez JF, Rosa C. Reverse transcriptase recombinase polymerase amplification for detection of tomato spotted wilt orthotospovirus from crude plant extracts. Sci Rep 2023; 13:9024. [PMID: 37270652 DOI: 10.1038/s41598-023-35343-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Virus detection in early stages of infection could prove useful for identification and isolation of foci of inoculum before its spread to the rest of susceptible individuals via vectoring insects. However, the low number of viruses present at the beginning of infection renders their detection and identification difficult and requires the use of highly sensitive laboratory techniques that are often incompatible with a field application. To obviate this challenge, utilized Recombinase Polymerase Amplification, an isothermal amplification technique that makes millions of copies of a predefined region in the genome, to detect tomato spotted wilt orthotospovirus in real time and at the end point. The reaction occurs isothermically and can be used directly from crude plant extracts without nucleic acid extraction. Notably, a positive result can be seen with the naked eye as a flocculus made of newly synthesized DNA and metallic beads. The objective of the procedure is to create a portable and affordable system that can isolate and identify viruses in the field, from infected plants and suspected insect vectors, and can be used by scientists and extension managers for making informed decisions for viral management. Results can be obtained in situ without the need of sending the samples to a specialized lab.
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Affiliation(s)
- Juan Francisco Iturralde Martinez
- Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, University Park, 16802, USA.
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, University Park, 16802, USA
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26
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Zhang H, Wang F, Song W, Yang Z, Li L, Ma Q, Tan X, Wei Z, Li Y, Li J, Yan F, Chen J, Sun Z. Different viral effectors suppress hormone-mediated antiviral immunity of rice coordinated by OsNPR1. Nat Commun 2023; 14:3011. [PMID: 37230965 DOI: 10.1038/s41467-023-38805-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 05/13/2023] [Indexed: 05/27/2023] Open
Abstract
Salicylic acid (SA) and jasmonic acid (JA) are plant hormones that typically act antagonistically in dicotyledonous plants and SA and JA signaling is often manipulated by pathogens. However, in monocotyledonous plants, the detailed SA-JA interplay in response to pathogen invasion remains elusive. Here, we show that different types of viral pathogen can disrupt synergistic antiviral immunity mediated by SA and JA via OsNPR1 in the monocot rice. The P2 protein of rice stripe virus, a negative-stranded RNA virus in the genus Tenuivirus, promotes OsNPR1 degradation by enhancing the association of OsNPR1 and OsCUL3a. OsNPR1 activates JA signaling by disrupting the OsJAZ-OsMYC complex and boosting the transcriptional activation activity of OsMYC2 to cooperatively modulate rice antiviral immunity. Unrelated viral proteins from different rice viruses also interfere with the OsNPR1-mediated SA-JA interplay to facilitate viral pathogenicity, suggesting that this may be a more general strategy in monocot plants. Overall, our findings highlight that distinct viral proteins convergently obstruct JA-SA crosstalk to facilitate viral infection in monocot rice.
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Affiliation(s)
- Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fengmin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Weiqi Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zihang Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Qiang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xiaoxiang Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Junmin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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27
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Viswanath KK, Kuo SY, Tu CW, Hsu YH, Huang YW, Hu CC. The Role of Plant Transcription Factors in the Fight against Plant Viruses. Int J Mol Sci 2023; 24:ijms24098433. [PMID: 37176135 PMCID: PMC10179606 DOI: 10.3390/ijms24098433] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.
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Affiliation(s)
- Kotapati Kasi Viswanath
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Song-Yi Kuo
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chin-Wei Tu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
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28
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Alazem M, Bwalya J, Pai H, Yu J, Cam HC, Burch-Smith T, Kim KH. Viral synergism suppresses R gene-mediated resistance by impairing downstream defense mechanisms in soybean. PLANT PHYSIOLOGY 2023:kiad255. [PMID: 37099452 PMCID: PMC10400036 DOI: 10.1093/plphys/kiad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/24/2023] [Accepted: 04/24/2023] [Indexed: 06/19/2023]
Abstract
Viral synergism occurs when mixed infection of a susceptible plant by two or more viruses leads to increased susceptibility to at least one of the viruses. However, the ability of one virus to suppress R gene-controlled resistance against another virus has never been reported. In soybean (Glycine max) extreme resistance (ER) against soybean mosaic virus (SMV), governed by the Rsv3 R-protein, manifests a swift asymptomatic resistance against the avirulent strain SMV-G5H. Still, the mechanism by which Rsv3 confers ER is not fully understood. Here, we show that viral synergism broke this resistance by impairing downstream defense mechanisms triggered by Rsv3 activation. We found that activation of the antiviral RNA silencing pathway and the proimmune mitogen-activated protein kinase 3 (MAPK3), along with the suppression of the proviral MAPK6, are hallmarks of Rsv3-mediated ER against SMV-G5H. Surprisingly, infection with bean pod mottle virus (BPMV) disrupted this ER, allowing SMV-G5H to accumulate in Rsv3-containing plants. BPMV subverted downstream defenses by impairing the RNA silencing pathway and activating MAPK6. Further, BPMV reduced the accumulation of virus-related siRNAs and increased the virus-activated siRNA that targeted several defense-related nucleotide-binding leucine-rich-repeat receptors (NLRs) genes through the action of the suppression of RNA-silencing activities encoded in its large and small coat protein subunits. These results illustrate that viral synergism can result from abolishing highly specific R gene resistance by impairing active mechanisms downstream of the R gene.
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Affiliation(s)
- Mazen Alazem
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - John Bwalya
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jisuk Yu
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Huong Chu Cam
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | | | - Kook-Hyung Kim
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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29
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Norberg A, Susi H, Sallinen S, Baran P, Clark NJ, Laine AL. Direct and indirect viral associations predict coexistence in wild plant virus communities. Curr Biol 2023; 33:1665-1676.e4. [PMID: 37019108 DOI: 10.1016/j.cub.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/17/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023]
Abstract
Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.
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Affiliation(s)
- Anna Norberg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7034 Trondheim, Norway.
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Pezhman Baran
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Nicholas J Clark
- School of Veterinary Science, Faculty of Science, University of Queensland, Gatton, QL 4343, Australia
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
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30
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Uchiyama S, Imamura Y, Matsuura T. A thermal cycler-based, homogenization-free plant total nucleic acid extraction method for plant viruses and viroids assay. J Virol Methods 2023; 313:114666. [PMID: 36539042 DOI: 10.1016/j.jviromet.2022.114666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
In this study, we report a plant total nucleic acid (TNA) extraction method for nucleic acid (NA)-based assays of plant viruses and viroids. This method combines NA release by incubating sliced plant tissue in solution and NA purification using silica spin column. The method is performed using a thermal cycler and microcentrifuge and does not involve tissue homogenization. For a wide range of plant species, TNA can be extracted from petioles, midribs, and stems, in 30 min. PCR/RT-PCR assays using extracts from this method detected all three DNA viruses, 14 RNA viruses, and 4 viroids tested and plant internal controls were also available. This method does not involve hazardous chemicals, is cost-effective. The method is readily implemented in various laboratories, a simple, rapid, and labor-saving option for NA-based assays of plant viruses and viroids.
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Affiliation(s)
- Shuichi Uchiyama
- Narita Sub-station, Yokohama Plant Protection Station, 2159, Aza Tennamino, Komaino, Narita 282-0021, Japan.
| | - Yuya Imamura
- Tsukuba Farm, Yokohama Plant Protection Station, 1-7, Nagamine, Tsukuba 305-0052, Japan
| | - Takayuki Matsuura
- Research Division, Yokohama Plant Protection Station, 1-16-10, Shin Yamashita, Naka-ku, Yokohama 231-0801, Japan
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31
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Song L, Jiao Y, Song H, Shao Y, Zhang D, Ding C, An D, Ge M, Li Y, Shen L, Wang F, Yang J. NbMLP43 Ubiquitination and Proteasomal Degradation via the Light Responsive Factor NbBBX24 to Promote Viral Infection. Cells 2023; 12:cells12040590. [PMID: 36831257 PMCID: PMC9954743 DOI: 10.3390/cells12040590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) plays an important role in virus-host interactions. However, the mechanism by which the UPS is involved in innate immunity remains unclear. In this study, we identified a novel major latex protein-like protein 43 (NbMLP43) that conferred resistance to Nicotiana benthamiana against potato virus Y (PVY) infection. PVY infection strongly induced NbMLP43 transcription but decreased NbMLP43 at the protein level. We verified that B-box zinc finger protein 24 (NbBBX24) interacted directly with NbMLP43 and that NbBBX24, a light responsive factor, acted as an essential intermediate component targeting NbMLP43 for its ubiquitination and degradation via the UPS. PVY, tobacco mosaic virus, (TMV) and cucumber mosaic virus (CMV) infections could promote NbMLP43 ubiquitination and proteasomal degradation to enhance viral infection. Ubiquitination occurred at lysine 38 (K38) within NbMLP43, and non-ubiquitinated NbMLP43(K38R) conferred stronger resistance to RNA viruses. Overall, our results indicate that the novel NbMLP43 protein is a target of the UPS in the competition between defense and viral anti-defense and enriches existing theoretical studies on the use of UPS by viruses to promote infection.
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Affiliation(s)
- Liyun Song
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yubing Jiao
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Hongping Song
- Hubei Engineering Research Center for Pest Forewarning and Management, Agricultural College, Yangtze University, Jingzhou 434025, China
| | - Yuzun Shao
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Daoshun Zhang
- Hubei Engineering Research Center for Pest Forewarning and Management, Agricultural College, Yangtze University, Jingzhou 434025, China
| | - Chengying Ding
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Dong An
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ming Ge
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (F.W.); (J.Y.)
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (F.W.); (J.Y.)
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Zlobin N, Taranov V. Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses. FRONTIERS IN PLANT SCIENCE 2023; 14:1041868. [PMID: 36844044 PMCID: PMC9950400 DOI: 10.3389/fpls.2023.1041868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Potyviruses are the largest group of plant-infecting RNA viruses that affect a wide range of crop plants. Plant resistance genes against potyviruses are often recessive and encode translation initiation factors eIF4E. The inability of potyviruses to use plant eIF4E factors leads to the development of resistance through a loss-of-susceptibility mechanism. Plants have a small family of eIF4E genes that encode several isoforms with distinct but overlapping functions in cell metabolism. Potyviruses use distinct eIF4E isoforms as susceptibility factors in different plants. The role of different members of the plant eIF4E family in the interaction with a given potyvirus could differ drastically. An interplay exists between different members of the eIF4E family in the context of plant-potyvirus interactions, allowing different eIF4E isoforms to modulate each other's availability as susceptibility factors for the virus. In this review, possible molecular mechanisms underlying this interaction are discussed, and approaches to identify the eIF4E isoform that plays a major role in the plant-potyvirus interaction are suggested. The final section of the review discusses how knowledge about the interaction between different eIF4E isoforms can be used to develop plants with durable resistance to potyviruses.
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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Lu Q, Luo X, Yang X, Zhou T, Zhang Y, Lan Y, Zhang D, Zheng L, Li Y, Li L, Zhang S, Liu Y. CRISPR/Cas9-mediated gene editing of vacuolar ATPase subunit d mediates phytohormone biosynthesis and virus resistance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1122978. [PMID: 36818855 PMCID: PMC9929465 DOI: 10.3389/fpls.2023.1122978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Vacuolar ATPases (V-ATPases) are proton pumps for proton translocation across membranes that utilize energy derived from ATP hydrolysis; OsV-ATPase subunit d (OsV-ATPase d) is part of an integral, membrane-embedded V0 complex in the V-ATPase complex. Whether OsV-ATPase d is involved in phytohormone biosynthesis and resistance in rice remains unknown. The knockout mutants of OsV-ATPase d in rice were generated using the CRISPR/Cas9 system, and mutation of OsV-ATPase d did not show any detrimental effect on plant growth or yield productivity. Transcriptomic results showed that OsV-ATPase d is probably involved in mediating the biosynthesis of plant hormones and resistance in rice. Compared to wild type, mutation of OsV-ATPase d significantly increased JA and ABA biosynthesis and resistance against Southern rice black-streaked dwarf virus (SRBSDV), but it decreased resistance against Rice stripe virus (RSV) in rice. The data presented in this study reveal that OsV-ATPase d mediates phytohormone biosynthesis and virus resistance in rice and can be selected as a potential target for resistance breeding in rice.
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Affiliation(s)
- Qinghua Lu
- Longping Branch of Biology College, Hunan University, Changsha, China
| | - Xiangwen Luo
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiao Yang
- Longping Branch of Biology College, Hunan University, Changsha, China
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yu Zhang
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ying Lan
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Deyong Zhang
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Limin Zheng
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yixin Li
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Li Li
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Songbai Zhang
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yong Liu
- Longping Branch of Biology College, Hunan University, Changsha, China
- State Key Laboratory of Hybird Rice, Hunan Academy of Agricultural Sciences, Changsha, China
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The rising threat of geminiviruses: molecular insights into the disease mechanism and mitigation strategies. Mol Biol Rep 2023; 50:3835-3848. [PMID: 36701042 DOI: 10.1007/s11033-023-08266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Geminiviruses are among the most threatening emerging plant viruses, accountable for a huge loss to agricultural production worldwide. These viruses have been responsible for some serious outbreaks during the last few decades across different parts of the world. Sincere efforts have been made to regulate the disease incidence by incorporating a multi-dimensional approach, and this process has been facilitated greatly by the advent of molecular techniques. But, the mixed infection due to the polyphagous nature of vectors results in viral recombination followed by the emergence of novel viral strains which thus renders the existing mitigation strategies ineffective. Hence, a multifaceted insight into the molecular mechanism of the disease is really needed to understand the regulatory points; much has been done in this direction during the last few years. The present review aims to explore all the latest developments made so far and to organize the information in a comprehensive manner so that some novel hypotheses for controlling the disease may be generated. METHODS AND RESULTS Starting with the background information, diverse genera of geminiviruses are listed along with their pathological and economic impacts. A comprehensive and detailed mechanism of infection is elaborated to study the interactions between vector, host, and virus at different stages in the life cycle of geminiviruses. Finally, an effort isalso made to analyze the progress made at the molecular level for the development of various mitigation strategies and suggest more effective and better approaches for controlling the disease. CONCLUSION The study has provided a thorough understanding of molecular mechanism of geminivirus infection.
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Biniaz Y, Khalesi M, Niazi A, Afsharifar A. Purification of an antiviral protein from the seeds of quinoa (Chenopodium quinoa Willd.) and characterization of its antiviral properties. Amino Acids 2023; 55:19-31. [PMID: 36348073 DOI: 10.1007/s00726-022-03200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/14/2022] [Indexed: 11/09/2022]
Abstract
Plant viral pathogens cause damaging diseases in many agriculture systems, and emerging viral infections are a serious threat for providing adequate food to a continuously growing population. Recent studies of biogenic substances have provided new opportunities for producing novel antiviral agents. The present work has been conducted to evaluate the antiviral activity of quinoa (Chenopodium quinoa Willd.) seeds crude extract. The antiviral activity was retained in different buffer solutions of various pH ranges (5.2-8.5) and remained after the diafiltration process. The putative virus inhibitor was sensitive to treatment with sodium dodecyl sulfate and trichloroacetic acid. An antiviral protein with ~ 25 kDa molecular weight was isolated from the seed quinoa extract using ammonium sulfate precipitation, anion and cation exchange chromatography. The purified protein (Quinoin-I) significantly inhibited TMV on tobacco leaves with an IC50 value at a 6.81 μg/ml concentration. Enzyme activity assay revealed the RNase activity of Quinoin-I, and this feature was retained in the presence of β-mercaptoethanol and ethylene diamine tetraacetic acid. This antiviral protein has been shown as a promising leading molecule for further development as a novel antiviral agent.
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Affiliation(s)
- Yaser Biniaz
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammadreza Khalesi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Biological Sciences, School of Natural Sciences, University of Limerick, Limerick, Ireland
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran.
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Systematic mutagenesis of Polerovirus protein P0 reveals distinct and overlapping amino acid functions in Nicotiana glutinosa. Virology 2023; 578:24-34. [PMID: 36462495 DOI: 10.1016/j.virol.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022]
Abstract
The protein P0 serves as the viral suppressor of RNA silencing (VSR) for poleroviruses, but elicits the hypersensitive response (HR) in specific Nicotiana species. We subjected P0 proteins from turnip yellows virus (P0Tu) and potato leafroll virus (P0PL) to serial deletion and performed extensive site-directed mutagenesis of P0Tu. Most deletions of the N-terminus and many substitution mutations disrupted both HR elicitation and VSR activity. Two conserved blocks of amino acid residues were found to be associated with HR. A double lysine to arginine substitution in HR-specific block 1 caused P0Tu to elicit a more robust HR. Conversely, deletion or mutation of block 2 in the C-terminus preserved VSR activity, but impaired HR elicitation, allowing virus escape from Nicotiana glutinosa resistance when expressed in the heterologous potato virus X vector. Our observations suggest that P0 residues responsible for suppressing RNA silencing and eliciting HR have overlapping, but distinct functions.
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Dai A, Zheng Z, Huang Y, Yu L, Wang Z, Jian Wu. Hydrazone modification of non-food natural product sclareolide as potential agents for plant disease. Heliyon 2022; 8:e12391. [PMID: 36636204 PMCID: PMC9830171 DOI: 10.1016/j.heliyon.2022.e12391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/30/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Plant diseases and their drug resistance pose a serious threat to agricultural production. One way to solve this problem is to discover new and efficient botanical pesticides. Herein, a series of novel hydrazide-hydrazone-containing sesquiterpenoid derivatives were synthesized by simply modifying the structure of the non-food natural product sclareolide. The biological activity results illustrated that compared to ningnanmycin (39.2 μg/mL), compound Z28 had the highest antiviral activity against tobacco mosaic virus (TMV), and the concentration for 50% of maximal effect (EC50) of its inactivation activity was 38.7 μg/mL, followed by compound Z14 (40.6 μg/mL). Transmission electron microscopy (TEM) demonstrated that TMVs treated with compounds Z14 and Z28 were broken into rods of different lengths, and their external morphology was fragmented or even severely fragmented. Autodocking and molecular dynamics (MD) simulations indicated that compound Z28 had a strong affinity for tobacco mosaic virus coat protein (TMV-CP), with a higher binding energy of -8.25 kcal/mol compared to ningnanmycin (-6.79 kcal/mol). The preliminary mechanism revealed that compound Z28 can achieve an antiviral effect by targeting TMV-CP, rendering TMV unable to self-assemble and replicate, and might be a candidate for a novel plant antiviral agent. Furthermore, the curative and protective activities of compound Z22 (EC50 = 16.1 μg/mL) against rice bacterial blight were 51.3% and 50.8%, respectively. Its control effect was better than that of bismerthiazol (BT) and thiadiazole copper (TC), compound Z22 that can be optimized as an active molecule.
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Zhao K, Liu SS, Wang XW, Yang JG, Pan LL. Manipulation of Whitefly Behavior by Plant Viruses. Microorganisms 2022; 10:microorganisms10122410. [PMID: 36557663 PMCID: PMC9782533 DOI: 10.3390/microorganisms10122410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Whiteflies of the Bemisia tabaci complex transmit hundreds of plant viruses belonging to the genera Begomovirus and Crinivirus, among others. Tripartite interactions of whitefly-virus-plant frequently occur during virus infection and transmission. Specifically, virus transmission-related behavior of whitefly, such as preference and feeding, may be altered by viruses and thus exert significant impacts on the outcome of virus spread and epidemics. Here, we provide an overview on the current understanding of the manipulation of whitefly behavior by plant viruses. Plant viruses can significantly modulate whitefly preference and feeding behavior, either directly or in a plant-mediated manner. In general, non-viruliferous whiteflies tend to prefer virus-infected plants, and viruliferous whiteflies are more likely to prefer uninfected plants. In most cases, virus infection of plants and/or whitefly seems to exhibit positive or no effects on whitefly feeding on plants. The significance and evolution of these patterns are then discussed. Finally, we suggest several future directions of research, such as the exploration of temporal dynamics and the dissection of underlying mechanisms of virus-induced changes in whitefly behavior.
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Affiliation(s)
- Kai Zhao
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Sheng Liu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin-Guang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (J.-G.Y.); (L.-L.P.)
| | - Li-Long Pan
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
- Correspondence: (J.-G.Y.); (L.-L.P.)
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Hilaire J, Tindale S, Jones G, Pingarron-Cardenas G, Bačnik K, Ojo M, Frewer LJ. Risk perception associated with an emerging agri-food risk in Europe: plant viruses in agriculture. AGRICULTURE & FOOD SECURITY 2022; 11:21. [PMID: 35310134 PMCID: PMC8917942 DOI: 10.1186/s40066-022-00366-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Research into public risk perceptions associated with emerging risks in agriculture and supply chains has focused on technological risks, zoonotic diseases, and food integrity, but infrequently on naturally occurring diseases in plants. Plant virus infections account for global economic losses estimated at $30 billion annually and are responsible for nearly 50% of plant diseases worldwide, threatening global food security. This research aimed to understand public perceptions of emerging risks and benefits associated with plant viruses in agriculture in Belgium, Slovenia, Spain, and the UK.
Methods
Online qualitative semi-structured interviews with 80 European consumers were conducted, including 20 participants in each of Belgium, Slovenia, the UK, and Spain. Microsoft Streams was used to transcribe the interview data, and NVivo was utilized to code the transcripts and analyze the data.
Results
The results indicate that, while study participants were relatively unfamiliar with the plant viruses and their potential impacts, plant viruses evoked perceived risks in a similar way to other emerging risks in the agri-food sector. These included risks to environment and human health, and the economic functioning of the relevant supply chain. Some participants perceived both risks and benefits to be associated with plant viruses. Benefits were perceived to be associated with improved plant resistance to viruses.
Conclusions
The results provide the basis for risk regulation, policy, and communication developments. Risk communication needs to take account of both risk and benefit perceptions, as well as the observation that plant viruses are perceived as an emerging, rather than an established, understood, and controlled risk. Some participants indicated the need for risk–benefit communication strategies to be developed, including information about the impacts of the risks, and associated mitigation strategies. Participants perceived that responsibility for control of plant viruses should be conferred on actors within the supply chain, in particular primary producers, although policy support (for example, financial incentivization) should be provided to improve their motivation to instigate risk mitigation activities.
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Bagchi R, Tinker-Kulberg R, Salehin M, Supakar T, Chamberlain S, Ligaba-Osena A, Josephs EA. Polyvalent guide RNAs for CRISPR antivirals. iScience 2022; 25:105333. [PMID: 36325075 PMCID: PMC9618770 DOI: 10.1016/j.isci.2022.105333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/13/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
CRISPR effector Cas13 recognizes and degrades RNA molecules that are complementary to its guide RNA (gRNA) and possesses potential as an antiviral biotechnology because it can degrade viral mRNA and RNA genomes. Because multiplexed targeting is a critical strategy to improve viral suppression, we developed a strategy to design of gRNAs where individual gRNAs have maximized activity at multiple viral targets, simultaneously, by exploiting the molecular biophysics of promiscuous target recognition by Cas13. These "polyvalent" gRNA sequences ("pgRNAs") provide superior antiviral elimination across tissue/organ scales in a higher organism (Nicotiana benthamiana) compared to conventionally-designed gRNAs-reducing detectable viral RNA by >30-fold, despite lacking perfect complementarity with either of their targets and, when multiplexed, reducing viral RNA by >99.5%. Pairs of pgRNA-targetable sequences are abundant in the genomes of RNA viruses, and this work highlights the need for specific approaches to the challenges of targeting viruses in eukaryotes using CRISPR.
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Affiliation(s)
- Rammyani Bagchi
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Rachel Tinker-Kulberg
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Mohammad Salehin
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Tinku Supakar
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Sydney Chamberlain
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Ayalew Ligaba-Osena
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Eric A. Josephs
- Department of Nanoscience, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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Juškytė AD, Mažeikienė I, Stanys V. Analysis of R Genes Related to Blackcurrant Reversion Virus Resistance in the Comparative Transcriptome of Ribes nigrum cv. Aldoniai. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223137. [PMID: 36432866 PMCID: PMC9692259 DOI: 10.3390/plants11223137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 05/14/2023]
Abstract
Blackcurrant reversion virus (BRV) is the most destructive mite-transmitted pathogen in blackcurrants. The understanding of the resistance to BRV is limited, hindering and delaying the selection process. To identify the resistance (R) gene for BRV resistance, a gene expression analysis based on de novo blackcurrant cv. Aldoniai comparative transcriptome analysis (mock- and BRV-inoculated samples at 2 and 4 days post-inoculation (dpi)) was performed. In this study, 111 annotated clusters associated with pathogenesis according to conservative R gene domains were identified. In virus-infected samples, only Cluster-12591.33361 showed significant expression at 4 dpi. The expression profiles of this cluster were significantly associated with the presence of BRV particles in plant tissues, making it a putative R gene in the dominant resistance strategy in the BRV-Ribes nigrum interaction. The newly identified gene R.nigrum_R belongs to the CC-NBS-LRR class and has 63.9% identity with RPM1 in Populus spp. This study provides new insights on dominant putative R genes related to resistance to BRV in R. nigrum, which could aid targeted research and genetic improvement in breeding programs of blackcurrants.
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Robertson G, Burger J, Campa M. CRISPR/Cas-based tools for the targeted control of plant viruses. MOLECULAR PLANT PATHOLOGY 2022; 23:1701-1718. [PMID: 35920132 PMCID: PMC9562834 DOI: 10.1111/mpp.13252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 05/15/2023]
Abstract
Plant viruses are known to infect most economically important crops and pose a major threat to global food security. Currently, few resistant host phenotypes have been delineated, and while chemicals are used for crop protection against insect pests and bacterial or fungal diseases, these are inefficient against viral diseases. Genetic engineering emerged as a way of modifying the plant genome by introducing functional genes in plants to improve crop productivity under adverse environmental conditions. Recently, new breeding technologies, and in particular the exciting CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) technology, was shown to be a powerful alternative to engineer resistance against plant viruses, thus has great potential for reducing crop losses and improving plant productivity to directly contribute to food security. Indeed, it could circumvent the "Genetic modification" issues because it allows for genome editing without the integration of foreign DNA or RNA into the genome of the host plant, and it is simpler and more versatile than other new breeding technologies. In this review, we describe the predominant features of the major CRISPR/Cas systems and outline strategies for the delivery of CRISPR/Cas reagents to plant cells. We also provide an overview of recent advances that have engineered CRISPR/Cas-based resistance against DNA and RNA viruses in plants through the targeted manipulation of either the viral genome or susceptibility factors of the host plant genome. Finally, we provide insight into the limitations and challenges that CRISPR/Cas technology currently faces and discuss a few alternative applications of the technology in virus research.
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Affiliation(s)
- Gaëlle Robertson
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
- Department of Experimental and Health SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Johan Burger
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
| | - Manuela Campa
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
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Agustika DK, Mercuriani I, Purnomo CW, Hartono S, Triyana K, Iliescu DD, Leeson MS. Fourier transform infrared spectrum pre-processing technique selection for detecting PYLCV-infected chilli plants. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121339. [PMID: 35537256 DOI: 10.1016/j.saa.2022.121339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Pre-processing is a crucial step in analyzing spectra from Fourier transform infrared (FTIR) spectroscopy because it can reduce unwanted noise and enhance system performance. Here, we present the results of pre-processing technique optimization to facilitate the detection of pepper yellow leaf curl virus (PYLCV)-infected chilli plants using FTIR spectroscopy. Optimization of a range of pre-processing techniques was undertaken, namely baseline correction, normalization (standard normal variate, vector, and min-max), and de-noising (Savitzky-Golay (SG) smoothing, 1st and 2 derivatives). The pre-processing was applied to the mid-infrared spectral range (4000 - 400 cm-1) and the biofingerprint region (1800 - 900 cm-1) then the discrete wavelet transform (DWT) was used for dimension reduction. The pre-processed data were then used as an input for classification using a multilayer perceptron neural network, a support vector machine, and linear discriminant analysis. The pre-processing method with the highest classification model accuracy was selected for the further use in the processing. It was seen that only the SG 1st derivative method applied to both wavenumber ranges could produce 100% accuracy. This result was supported by principal component analysis clustering. Thus, we have demonstrated that by using the right pre-processing technique, classification success can be increased, and the process simplified by optimization and minimization of the technique used.
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Affiliation(s)
- Dyah K Agustika
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; Department of Physics Education, Universitas Negeri Yogyakarta, Yogyakarta, 55281 Indonesia.
| | - Ixora Mercuriani
- Department of Biology Education, Universitas Negeri Yogyakarta, Yogyakarta, 55281 Indonesia
| | - Chandra W Purnomo
- Department of Chemical Engineering, Universitas Gadjah Mada, Sekip Utara Yogyakarta, 55281 Indonesia
| | - Sedyo Hartono
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada. Jl, Flora 1, Bulaksumur, Sleman 55281, Yogyakarta
| | - Kuwat Triyana
- Department of Physics, Universitas Gadjah Mada, Sekip Utara Yogyakarta, 55281 Indonesia
| | - Doina D Iliescu
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Mark S Leeson
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK.
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45
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McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
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Affiliation(s)
| | | | | | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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46
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Pan W, Li W, Liu L, Zhang H. Antiviral strategies: What can we learn from natural reservoirs? JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1849-1855. [PMID: 36103243 DOI: 10.1111/jipb.13362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Viruses cause many severe diseases in both plants and animals, urging us to explore new antiviral strategies. In their natural reservoirs, viruses live and replicate while causing mild or no symptoms. Some animals, such as bats, are the predicted natural reservoir of multiple viruses, indicating that they possess broad-spectrum antiviral capabilities. Mechanisms of host defenses against viruses are generally studied independently in plants and animals. In this article, we speculate that some antiviral strategies of natural reservoirs are conserved between kingdoms. To verify this hypothesis, we created null mutants of 10-formyltetrahydrofolate synthetase (AtTHFS), an Arabidopsis thaliana homologue of methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 (MTHFD1), which encodes a positive regulator of viral replication in bats. We found that disruption of AtTHFS enhanced plant resistance to three different types of plant viruses, including the tomato spotted wilt virus (TSWV), the cucumber mosaic virus (CMV) and the beet severe curly top virus (BSCTV). These results demonstrate a novel antiviral strategy for plant breeding. We further discuss the approaches used to identify and study natural reservoirs of plant viruses, especially those hosting many viruses, and highlight the possibility of discovering new antiviral strategies from them for plant molecular breeding and antiviral therapy.
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Affiliation(s)
- Wenbo Pan
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Weiwei Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Lijing Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Huawei Zhang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
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47
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Analysis of the Contribution of Intrinsic Disorder in Shaping Potyvirus Genetic Diversity. Viruses 2022; 14:v14091959. [PMID: 36146764 PMCID: PMC9504506 DOI: 10.3390/v14091959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 12/30/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are abundant in the proteome of RNA viruses. The multifunctional properties of these regions are widely documented and their structural flexibility is associated with the low constraint in their amino acid positions. Therefore, from an evolutionary stand point, these regions could have a greater propensity to accumulate non-synonymous mutations (NS) than highly structured regions (ORs, or 'ordered regions'). To address this hypothesis, we compared the distribution of non-synonymous mutations (NS), which we relate here to mutational robustness, in IDRs and ORs in the genome of potyviruses, a major genus of plant viruses. For this purpose, a simulation model was built and used to distinguish a possible selection phenomenon in the biological datasets from randomly generated mutations. We analyzed several short-term experimental evolution datasets. An analysis was also performed on the natural diversity of three different species of potyviruses reflecting their long-term evolution. We observed that the mutational robustness of IDRs is significantly higher than that of ORs. Moreover, the substitutions in the ORs are very constrained by the conservation of the physico-chemical properties of the amino acids. This feature is not found in the IDRs where the substitutions tend to be more random. This reflects the weak structural constraints in these regions, wherein an amino acid polymorphism is naturally conserved. In the course of evolution, potyvirus IDRs and ORs follow different evolutive paths with respect to their mutational robustness. These results have forced the authors to consider the hypothesis that IDRs and their associated amino acid polymorphism could constitute a potential adaptive reservoir.
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48
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Zhang S, Griffiths JS, Marchand G, Bernards MA, Wang A. Tomato brown rugose fruit virus: An emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide. MOLECULAR PLANT PATHOLOGY 2022; 23:1262-1277. [PMID: 35598295 PMCID: PMC9366064 DOI: 10.1111/mpp.13229] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
UNLABELLED Tomato brown rugose fruit virus (ToBRFV) is an emerging and rapidly spreading RNA virus that infects tomato and pepper, with tomato as the primary host. The virus causes severe crop losses and threatens tomato production worldwide. ToBRFV was discovered in greenhouse tomato plants grown in Jordan in spring 2015 and its first outbreak was traced back to 2014 in Israel. To date, the virus has been reported in at least 35 countries across four continents in the world. ToBRFV is transmitted mainly via contaminated seeds and mechanical contact (such as through standard horticultural practices). Given the global nature of the seed production and distribution chain, and ToBRFV's seed transmissibility, the extent of its spread is probably more severe than has been disclosed. ToBRFV can break down genetic resistance to tobamoviruses conferred by R genes Tm-1, Tm-2, and Tm-22 in tomato and L1 and L2 alleles in pepper. Currently, no commercial ToBRFV-resistant tomato cultivars are available. Integrated pest management-based measures such as rotation, eradication of infected plants, disinfection of seeds, and chemical treatment of contaminated greenhouses have achieved very limited success. The generation and application of attenuated variants may be a fast and effective approach to protect greenhouse tomato against ToBRFV. Long-term sustainable control will rely on the development of novel genetic resistance and resistant cultivars, which represents the most effective and environment-friendly strategy for pathogen control. TAXONOMY Tomato brown rugose fruit virus belongs to the genus Tobamovirus, in the family Virgaviridae. The genus also includes several economically important viruses such as Tobacco mosaic virus and Tomato mosaic virus. GENOME AND VIRION The ToBRFV genome is a single-stranded, positive-sense RNA of approximately 6.4 kb, encoding four open reading frames. The viral genomic RNA is encapsidated into virions that are rod-shaped and about 300 nm long and 18 nm in diameter. Tobamovirus virions are considered extremely stable and can survive in plant debris or on seed surfaces for long periods of time. DISEASE SYMPTOMS Leaves, particularly young leaves, of tomato plants infected by ToBRFV exhibit mild to severe mosaic symptoms with dark green bulges, narrowness, and deformation. The peduncles and calyces often become necrotic and fail to produce fruit. Yellow blotches, brown or black spots, and rugose wrinkles appear on tomato fruits. In pepper plants, ToBRFV infection results in puckering and yellow mottling on leaves with stunted growth of young seedlings and small yellow to brown rugose dots and necrotic blotches on fruits.
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Affiliation(s)
- Shaokang Zhang
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyThe University of Western OntarioLondonOntarioCanada
| | - Jonathan S. Griffiths
- London Research and Development CentreAgriculture and Agri‐Food CanadaVinelandOntarioCanada
| | - Geneviève Marchand
- Harrow Research and Development CentreAgriculture and Agri‐Food CanadaHarrowOntarioCanada
| | - Mark A. Bernards
- Department of BiologyThe University of Western OntarioLondonOntarioCanada
| | - Aiming Wang
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyThe University of Western OntarioLondonOntarioCanada
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49
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He HW, Wang FY, Zhang D, Chen CY, Xu D, Zhou H, Liu X, Xu G. Discovery of Novel α-Methylene-γ-Butyrolactone Derivatives Containing Vanillin Moieties as Antiviral and Antifungal Agents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10316-10325. [PMID: 35960686 DOI: 10.1021/acs.jafc.2c03632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
On the basis of the structure of nicotlactone A (L1), a series of novel α-methylene-γ-butyrolactone derivatives B1-B43 were designed and synthesized by structure simplification and active fragment replacement strategies, and their antiviral and antifungal activities were evaluated. The bioassay studies indicated that many target compounds possessed good to excellent antiviral activity against tobacco mosaic virus (TMV) and some of these compounds exhibited specific antifungal activities against Valsa mali and Fusarium graminearum. Compound B32 exhibited the best anti-TMV activity (inactivation effect, 88.9%; protection effect, 65.8%; curative effect, 52.8%) in vivo at 500 mg/L, which is significantly higher than that of commercial virucides ribavirin and ningnanmycin. The inhibition effect of compound B32 was also visualized by the inoculation test using green fluorescent protein (GFP)-labeled TMV. The preliminary antiviral mechanism of compound B32 was investigated. Transmission electron microscopy (TEM) showed that compound B32 could destroy the integrity of virus particles. Then, molecular docking and isothermal titration calorimetry (ITC) analysis further demonstrated that compound B32 exhibited a strong binding affinity to the TMV coat protein with a dissociation constant (Kd) of 3.06 μM, superior to ribavirin. Thus, we deduced that compound B32 may interfere with the self-assembly of TMV particles by binding TMV coat protein (CP). In addition, compound B28 showed good in vitro activity against F. graminearum with an inhibition rate of 90.9% at 50 mg/L, which was greater than that of fluxapyroxad (59.1%) but lower than that of the commercial fungicide carbendazim (96.8%). The present study provides support for the application of these α-methylene-γ-butyrolactone derivatives as novel antiviral and antifungal agents in crop protection.
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Affiliation(s)
- Hong-Wei He
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
| | - Fei-Yu Wang
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
| | - Danyang Zhang
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
| | - Cai-Yun Chen
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
| | - Dan Xu
- College of Chemistry & Pharmacy, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Shaanxi Key Laboratory of Natural Products & Chemical Biology, Yangling ,Shaanxi 712100, China
| | - Huan Zhou
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Shaanxi Key Laboratory of Natural Products & Chemical Biology, Yangling ,Shaanxi 712100, China
| | - Xili Liu
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Shaanxi Key Laboratory of Natural Products & Chemical Biology, Yangling ,Shaanxi 712100, China
| | - Gong Xu
- College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling ,Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Shaanxi Key Laboratory of Natural Products & Chemical Biology, Yangling ,Shaanxi 712100, China
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50
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Marqués MC, Sánchez-Vicente J, Ruiz R, Montagud-Martínez R, Márquez-Costa R, Gómez G, Carbonell A, Daròs JA, Rodrigo G. Diagnostics of Infections Produced by the Plant Viruses TMV, TEV, and PVX with CRISPR-Cas12 and CRISPR-Cas13. ACS Synth Biol 2022; 11:2384-2393. [PMID: 35793201 PMCID: PMC9295153 DOI: 10.1021/acssynbio.2c00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral infections in plants threaten food security. Thus, simple and effective methods for virus detection are required to adopt early measures that can prevent virus spread. However, current methods based on the amplification of the viral genome by polymerase chain reaction (PCR) require laboratory conditions. Here, we exploited the CRISPR-Cas12a and CRISPR-Cas13a/d systems to detect three RNA viruses, namely, Tobacco mosaic virus, Tobacco etch virus, and Potato virus X, in Nicotiana benthamiana plants. We applied the CRISPR-Cas12a system to detect viral DNA amplicons generated by PCR or isothermal amplification, and we also performed a multiplexed detection in plants with mixed infections. In addition, we adapted the detection system to bypass the costly RNA purification step and to get a visible readout with lateral flow strips. Finally, we applied the CRISPR-Cas13a/d system to directly detect viral RNA, thereby avoiding the necessity of a preamplification step and obtaining a readout that scales with the viral load. These approaches allow for the performance of viral diagnostics within half an hour of leaf harvest and are hence potentially relevant for field-deployable applications.
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Affiliation(s)
- María-Carmen Marqués
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Javier Sánchez-Vicente
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - Raúl Ruiz
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Roser Montagud-Martínez
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Rosa Márquez-Costa
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Gustavo Gómez
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Alberto Carbonell
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - José-Antonio Daròs
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - Guillermo Rodrigo
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
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